# Data and Code for "Towards a Biological State-Mediated Hamiltonian: A Preliminary Theoretical Model for Quantum Effects in Periodontal Low-Level Laser Therapy"

## Overview
This repository contains simulation data and code supporting the theoretical model presented in the manuscript titled "Towards a Biological State-Mediated Hamiltonian: A Preliminary Theoretical Model for Quantum Effects in Periodontal Low-Level Laser Therapy." The study explores quantum effects in low-level laser therapy (LLLT) applied to periodontal tissues using a two-level system (TLS) framework, grounded in open quantum systems theory. The model simulates laser-driven excitations and decoherence, integrating parameters from LLLT literature (e.g., wavelengths 600-1000 nm, fluences 1-10 J/cm²) to predict coherence timescales and energy transfer efficiencies. This work bridges quantum physics and clinical periodontology, laying groundwork for future experimental validation.

The data and code are provided to ensure reproducibility and to facilitate further research into quantum biophysics and photobiomodulation in dental applications. The manuscript is under review [pending DOI 10.5281/zenodo.17373323].

## Files

### Raw Data
- `TLS_HAMILTONIAN_SIMULATION_DATA.xlsx`: Initial simulation data for the TLS Hamiltonian model.
- `TLS_PARAMETRIC-SWEEP.xlsx`: Data from parametric sweeps over Rabi frequencies (Ω = [0.05, 0.1, 0.2, 0.5] MHz) and decoherence rates (γ = [0.05, 0.1, 0.2] MHz).
- `LLLT_QUANTUM_DYNAMICS.xlsx`: Quantum dynamics data specific to LLLT parameters.
- `tls_steady_state_populations.xlsx`: Steady-state excited population data (e.g., Table 1 from manuscript).
- `tls_coherence_decay_fits.xlsx`: Exponential fit parameters for coherence decay (e.g., Table 2 from manuscript).
- `tls_sample_time_series.xlsx`: Representative time-series excerpt (e.g., Table 4 from manuscript).
- `fig1_population_evolution_data.xlsx`: Raw data for Figure 1 (population evolution over 0-50 µs).
- `fig2_coherence_decay_data.xlsx`: Raw data for Figure 2 (coherence decay over 0-50 µs).

### Code
- `TLS_HAMILTONIAN_SIMULATION_DATA.ipynb`: Jupyter notebook for generating initial TLS simulation data.
- `TLS_PARAMETRIC-SWEEP.ipynb`: Notebook for parametric sweep simulations.
- `LLLT_QUANTUM_DYNAMICS_1.ipynb`, `LLLT_QUANTUM_DYNAMICS_2.ipynb`, `LLLT_QUANTUM_DYNAMICS_3.ipynb`: Three notebooks for TLS parameter setups under LLLT conditions (distinct setups for different parameter configurations).
- `TLS_DERIVED_DATASETS.ipynb`: Notebook for deriving datasets (e.g., regression, coherence fits).
- `STEADY-STATE_POPULATIONS_COHERENCE_DECAY_FITTING_TIME-SERIES_ANALYSIS.ipynb`: Combined notebook for steady-state, coherence decay fitting, and time-series analysis.
- `COHERENCE_DECAY.ipynb`: Notebook for specific coherence decay analysis.
- `fig1_population_evolution.py`: Python script to generate Figure 1.
- `fig2_coherence_decay.py`: Python script to generate Figure 2.

### Documentation
- `README.md`: This file, providing an overview, file descriptions, usage instructions, and licensing information.

## Usage Instructions
### Dependencies
- Python 3.x
- Libraries: QuTiP, NumPy, Pandas, Matplotlib
- Installation: Use `pip install qutip numpy pandas matplotlib` in a Python environment.

### Running Code
1. Clone or download this repository.
2. Ensure all `.xlsx` data files are in the same directory as the corresponding `.ipynb` or `.py` files.
3. Open `.ipynb` files in Jupyter Notebook or JupyterLab and run cells sequentially.
   - Example: Run `TLS_HAMILTONIAN_SIMULATION_DATA.ipynb` to replicate initial simulations.
4. Execute `.py` files using Python (e.g., `python fig1_population_evolution.py`) to generate figures.
5. Adjust parameters (e.g., Ω, γ) in code as needed, referencing `TLS_PARAMETRIC-SWEEP.xlsx` for ranges.

### Data Structure
- Excel files are organized with columns (e.g., Time, Excited_Population, Coherence) and rows corresponding to simulation outputs.
- Full datasets (e.g., 500-1500 points) are provided; sample excerpts align with manuscript tables.

## License
This work is licensed under the Creative Commons Attribution 4.0 International (CC-BY 4.0) license. You are free to share and adapt the material for any purpose, including commercially, provided you give appropriate credit, provide a link to the license, and indicate if changes were made. See [https://creativecommons.org/licenses/by/4.0/](https://creativecommons.org/licenses/by/4.0/) for details.

## Citation
If you use this data or code, please cite the Zenodo DOI (10.5281/zenodo.17373323) and the associated manuscript once published. Example:
- [Dr Bugude Shiva Shankar]. Data and Code for "Towards a Biological State-Mediated Hamiltonian: A Preliminary Theoretical Model for Quantum Effects in Periodontal Low-Level Laser Therapy". Zenodo. [DOI 10.5281/zenodo.17373323]; 2025.
- [Dr Bugude Shiva Shankar]. Towards a Biological State-Mediated Hamiltonian: A Preliminary Theoretical Model for Quantum Effects in Periodontal Low-Level Laser Therapy.

## Contact
For questions or collaboration, contact [Dr Bugude Shiva Shankar/S.ggg@qu.edu.sa].

## Acknowledgements
I acknowledge my sons Saakshar & Saaransh for supporting this work.
